Contacts of the helix formed by residues 471 - 488 (chain A) in PDB entry 2R8J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PHE* 3.1 23.7 + + + +
469A GLN 3.8 0.4 - - - -
470A SER* 1.3 82.5 - - - +
472A GLU* 1.3 74.0 + - + +
473A LEU 2.9 4.8 - - - +
474A LEU* 2.9 29.2 + - + +
475A LYS* 2.9 28.0 + - + +
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A VAL* 3.8 2.6 - - + +
462A ALA 3.5 16.3 - - - +
463A TYR* 3.0 38.1 - - + +
464A LYS* 3.2 36.3 + - - +
468A PHE* 3.4 20.7 + - + +
471A HIS* 1.3 94.5 + - + +
473A LEU* 1.3 61.7 + - - +
475A LYS* 3.4 20.4 + - + +
476A VAL* 3.2 28.8 + - + +
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A CYS* 4.4 8.7 - - - -
423A LEU* 4.6 20.2 - - + -
424A THR* 4.9 3.6 - - - +
427A ILE* 4.7 3.6 - - + -
440A PRO* 4.7 8.3 - - + -
443A VAL* 3.6 33.6 - - + +
461A VAL* 4.2 8.7 - - + +
463A TYR* 4.3 11.5 - - - +
468A PHE 4.5 1.4 + - - -
469A GLN 3.9 27.4 - - - +
470A SER* 4.9 0.9 - - - -
471A HIS 2.9 2.8 - - - +
472A GLU* 1.3 79.9 - - - +
474A LEU* 1.3 61.4 + - - +
476A VAL* 3.4 3.3 + - - +
477A GLY* 3.1 17.7 + - - -
501A MET* 3.7 15.6 - - - +
503A ILE* 4.1 19.1 - - + -
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 4.8 1.3 - - + +
416A LEU* 3.7 40.4 - - + -
417A GLU* 4.0 24.0 - - + +
420A CYS* 3.4 20.3 - - + -
470A SER 5.1 2.9 - - - +
471A HIS* 2.9 18.4 + - + +
473A LEU* 1.3 78.8 - - - +
475A LYS* 1.3 65.4 + - - +
477A GLY 3.2 1.1 + - - +
478A ILE* 2.9 49.3 + - + +
501A MET* 4.6 1.1 - - + -
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 5.9 3.6 - - - +
471A HIS* 2.9 29.0 + - + +
472A GLU* 3.4 26.0 + - + +
473A LEU 3.2 0.2 - - - -
474A LEU* 1.3 78.5 - - - +
476A VAL* 1.3 63.9 + - + +
478A ILE* 3.5 11.5 + - - +
479A LYS* 3.4 17.0 + - - +
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL* 4.3 16.8 - - + -
459A GLY 5.1 0.4 - - - +
460A PRO 4.7 9.2 - - - +
461A VAL* 3.8 22.4 - - + -
462A ALA 4.9 2.7 - - - +
472A GLU* 3.2 15.6 + - + +
473A LEU 3.8 5.8 - - - +
475A LYS* 1.3 75.8 - - + +
477A GLY* 1.3 68.3 + - - +
479A LYS* 3.2 7.4 + - + +
480A PHE* 3.0 54.5 + - + -
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Residues in contact with GLY 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A LEU* 3.9 7.3 - - - +
443A VAL* 5.1 3.1 - - - +
445A ILE* 4.0 14.6 - - - +
473A LEU 3.1 15.3 + - - -
474A LEU 3.2 4.0 + - - -
476A VAL* 1.3 76.7 - - - +
478A ILE* 1.3 56.8 + - - +
480A PHE* 3.3 2.5 + - - +
481A VAL* 2.8 30.1 + - - +
501A MET* 4.1 18.8 - - - -
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ILE* 3.8 37.5 - - + -
416A LEU* 3.9 6.7 - - + +
474A LEU* 2.9 41.9 + - + +
475A LYS* 3.7 9.0 - - - +
476A VAL 3.2 0.2 - - - -
477A GLY* 1.3 72.4 - - - +
479A LYS* 1.3 67.4 + - - +
481A VAL* 3.0 7.9 - - - +
482A THR* 2.8 35.9 + - - +
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Residues in contact with LYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 4.0 12.9 - - - +
475A LYS 3.4 9.7 + - - +
476A VAL* 3.2 12.1 + - + +
478A ILE* 1.3 75.9 - - - +
480A PHE* 1.3 63.0 + - + +
482A THR* 2.8 10.0 + - - -
483A ASP* 2.6 68.8 + - - +
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Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A VAL* 4.2 7.9 - - + -
444A SER* 4.9 0.9 - - - -
445A ILE* 3.8 19.5 - - + -
457A LYS* 3.0 57.0 - - + -
458A SER* 3.4 4.5 - - - -
459A GLY* 3.2 40.8 - - - -
460A PRO* 5.5 1.1 - - + -
476A VAL* 3.0 38.0 + - + +
477A GLY 3.5 7.6 - - - +
479A LYS* 1.3 91.6 - - + +
481A VAL* 1.3 63.7 + - - +
483A ASP* 3.2 2.3 + - - +
484A LEU* 3.1 30.6 + - - +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ILE* 3.7 13.7 - - + +
412A CYS* 3.4 34.3 - - + -
413A ILE* 4.5 7.0 - - + -
416A LEU* 3.6 22.7 - - + -
445A ILE* 4.5 9.1 - - + +
447A LEU* 5.3 6.3 - - + -
477A GLY 2.8 19.3 + - - +
478A ILE* 3.0 20.2 - - - +
480A PHE* 1.3 72.5 - - - +
482A THR* 1.3 57.9 + - - +
484A LEU* 3.6 9.4 + - - +
485A ASP* 3.2 23.7 + - - +
493A TYR* 4.6 1.6 + - - +
499A LEU* 4.6 14.6 - - + -
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Residues in contact with THR 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ILE* 3.9 21.7 - - + +
413A ILE* 5.2 0.5 - - - +
478A ILE* 2.8 29.9 + - - +
479A LYS* 3.2 13.2 - - - -
481A VAL* 1.3 77.3 - - - +
483A ASP* 1.3 67.0 + - - +
484A LEU 3.2 0.2 - - - -
485A ASP* 3.2 13.3 + - + +
486A ILE* 3.3 24.1 + - + +
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A LYS* 3.1 27.4 + - + +
479A LYS* 2.6 64.4 + - - +
480A PHE 3.7 4.7 - - - +
482A THR* 1.3 78.4 - - - +
484A LEU* 1.3 59.1 + - + +
486A ILE* 3.4 12.0 + - - +
487A LYS* 3.1 23.4 + - - +
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ILE* 4.1 24.9 - - + +
447A LEU* 4.5 13.2 - - + -
455A TYR* 4.1 5.5 - - + -
456A ARG* 4.1 15.7 - - - +
457A LYS* 4.1 30.5 - - + +
480A PHE 3.1 20.9 + - - +
481A VAL* 3.8 5.2 - - - +
483A ASP* 1.3 74.5 - - - +
485A ASP* 1.3 65.7 + - - +
486A ILE 3.1 1.8 - - - -
487A LYS* 3.1 43.4 + - + +
488A GLY 3.3 9.7 + - - -
493A TYR* 3.3 24.5 + - + +
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.8 22.3 - - + +
481A VAL 3.2 14.9 + - - +
482A THR* 3.2 12.8 + - + +
484A LEU* 1.3 77.2 - - - +
486A ILE* 1.3 63.3 + - - +
488A GLY 3.8 9.0 + - - +
489A LYS* 3.4 36.6 + - - +
493A TYR* 3.7 10.6 + - - -
494A TYR* 2.7 37.9 + - - +
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Residues in contact with ILE 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A THR* 3.3 23.5 + - + +
483A ASP* 3.6 13.7 - - - +
484A LEU 3.1 0.6 - - - -
485A ASP* 1.3 80.9 - - - +
487A LYS* 1.3 63.3 + - - +
488A GLY 3.2 2.9 + - - -
489A LYS* 3.8 23.9 + - + +
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Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 3.6 32.3 - - + +
456A ARG 4.6 11.9 + - - +
483A ASP 3.1 16.6 + - - +
484A LEU* 3.1 28.1 + - + +
486A ILE* 1.3 78.4 - - - +
488A GLY* 1.3 55.3 + - - +
489A LYS 3.8 1.3 + - - -
491A LYS* 4.6 9.0 - - - +
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 4.4 6.5 - - - -
484A LEU 3.3 10.8 + - - -
485A ASP 4.0 6.1 - - - +
486A ILE 3.2 0.8 - - - -
487A LYS* 1.3 80.6 - - - +
489A LYS* 1.3 61.1 + - - +
490A ASN 3.6 1.1 - - - -
491A LYS* 4.0 17.8 - - - +
493A TYR* 3.7 36.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il